OpenRaiser/Intern-Atlas huggingface dataset:
Higher-order, generically complete, continuous, and polynomial-time isometry invariants of periodic sets
Venue: arXiv cs.CG 2025
Year: 2025

Periodic point sets model all solid crystalline materials (crystals) whose atoms can be considered zero-sized points with or without atomic types. This paper addresses the fundamental problem of checking whether claimed crystals are novel, not noisy perturbations of known materials obtained by unrealistic atomic replacements. Such near-duplicates have skewed ground-truth because past comparisons relied on unstable cells and symmetries. The proposed Lipschitz continuity under noise is a new essential requirement for machine learning on any data objects that have ambiguous representations and live in continuous spaces. For periodic point sets under isometry (any distance-preserving transformation), we designed invariants that distinguish all known counter-examples to the completeness of past descriptors and detect thousands of (near-)duplicates in large high-profile databases of crystals within two days on a modest desktop computer.
Vulnerable Agent Identification in Large-Scale Multi-Agent Reinforcement Learning
Venue: arXiv cs.MA 2025
Year: 2025

Partial agent failure becomes inevitable when systems scale up, making it crucial to identify the subset of agents whose compromise would most severely degrade overall performance. In this paper, we study this Vulnerable Agent Identification (VAI) problem in large-scale multi-agent reinforcement learning (MARL). We frame VAI as a Hierarchical Adversarial Decentralized Mean Field Control (HAD-MFC), where the upper level involves an NP-hard combinatorial task of selecting the most vulnerable agents, and the lower level learns worst-case adversarial policies for these agents using mean-field MARL. The two problems are coupled together, making HAD-MFC difficult to solve. To solve this, we first decouple the hierarchical process by Fenchel-Rockafellar transform, resulting a regularized mean-field Bellman operator for upper level that enables independent learning at each level, thus reducing computational complexity. We then reformulate the upper-level combinatorial problem as a MDP with dense rewards from our regularized mean-field Bellman operator, enabling us to sequentially identify the most vulnerable agents by greedy and RL algorithms. This decomposition provably preserves the optimal solution of the original HAD-MFC. Experiments show our method effectively identifies more vulnerable agents in large-scale MARL and the rule-based system, fooling system into worse failures, and learns a value function that reveals the vulnerability of each agent.
WorldForge: Unlocking Emergent 3D/4D Generation in Video Diffusion Model via Training-Free Guidance
Venue: arXiv cs.GR 2025
Year: 2025

Recent video diffusion models show immense potential for spatial intelligence tasks due to their rich world priors, but this is undermined by limited controllability, poor spatial-temporal consistency, and entangled scene-camera dynamics. Existing solutions, such as model fine-tuning and warping-based repainting, struggle with scalability, generalization, and robustness against artifacts. To address this, we propose WorldForge, a training-free, inference-time framework composed of three tightly coupled modules. 1) Intra-Step Recursive Refinement injects fine-grained trajectory guidance at denoising steps through a recursive correction loop, ensuring motion remains aligned with the target path. 2) Flow-Gated Latent Fusion leverages optical flow similarity to decouple motion from appearance in the latent space and selectively inject trajectory guidance into motion-related channels. 3) Dual-Path Self-Corrective Guidance compares guided and unguided denoising paths to adaptively correct trajectory drift caused by noisy or misaligned structural signals. Together, these components inject fine-grained, trajectory-aligned guidance without training, achieving both accurate motion control and photorealistic content generation. Our framework is plug-and-play and model-agnostic, enabling broad applicability across various 3D/4D tasks. Extensive experiments demonstrate that our method achieves state-of-the-art performance in trajectory adherence, geometric consistency, and perceptual quality, outperforming both training-intensive and inference-only baselines.
SMARTER: A Data-efficient Framework to Improve Toxicity Detection with Explanation via Self-augmenting Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

WARNING: This paper contains examples of offensive materials. To address the proliferation of toxic content on social media, we introduce SMARTER, we introduce SMARTER, a data-efficient two-stage framework for explainable content moderation using Large Language Models (LLMs). In Stage 1, we leverage LLMs' own outputs to generate synthetic explanations for both correct and incorrect labels, enabling alignment via preference optimization with minimal human supervision. In Stage 2, we refine explanation quality through cross-model training, allowing weaker models to align stylistically and semantically with stronger ones. Experiments on three benchmark tasks -- HateXplain, Latent Hate, and Implicit Hate -- demonstrate that SMARTER enables LLMs to achieve up to a 13.5% macro-F1 improvement over standard few-shot baselines while using only a fraction of the full training data. Our framework offers a scalable strategy for low-resource settings by harnessing LLMs' self-improving capabilities for both classification and explanation.
Maize Seedling Detection Dataset (MSDD): A Curated High-Resolution RGB Dataset for Seedling Maize Detection and Benchmarking with YOLOv9, YOLO11, YOLOv12 and Faster-RCNN
Venue: arXiv cs.CV 2025
Year: 2025

Accurate maize seedling detection is crucial for precision agriculture, yet curated datasets remain scarce. We introduce MSDD, a high-quality aerial image dataset for maize seedling stand counting, with applications in early-season crop monitoring, yield prediction, and in-field management. Stand counting determines how many plants germinated, guiding timely decisions such as replanting or adjusting inputs. Traditional methods are labor-intensive and error-prone, while computer vision enables efficient, accurate detection. MSDD contains three classes-single, double, and triple plants-capturing diverse growth stages, planting setups, soil types, lighting conditions, camera angles, and densities, ensuring robustness for real-world use. Benchmarking shows detection is most reliable during V4-V6 stages and under nadir views. Among tested models, YOLO11 is fastest, while YOLOv9 yields the highest accuracy for single plants. Single plant detection achieves precision up to 0.984 and recall up to 0.873, but detecting doubles and triples remains difficult due to rarity and irregular appearance, often from planting errors. Class imbalance further reduces accuracy in multi-plant detection. Despite these challenges, YOLO11 maintains efficient inference at 35 ms per image, with an additional 120 ms for saving outputs. MSDD establishes a strong foundation for developing models that enhance stand counting, optimize resource allocation, and support real-time decision-making. This dataset marks a step toward automating agricultural monitoring and advancing precision agriculture.
Conditional Prior-based Non-stationary Channel Estimation Using Accelerated Diffusion Models
Venue: arXiv cs.DC 2025
Year: 2025

Wireless channels in motion-rich urban microcell (UMi) settings are non-stationary; mobility and scatterer dynamics shift the distribution over time, degrading classical and deep estimators. This work proposes conditional prior diffusion for channel estimation, which learns a history-conditioned score to denoise noisy channel snapshots. A temporal encoder with cross-time attention compresses a short observation window into a context vector, which captures the channel's instantaneous coherence and steers the denoiser via feature-wise modulation. In inference, an SNR-matched initialization selects the diffusion step whose marginal aligns with the measured input SNR, and the process follows a shortened, geometrically spaced schedule, preserving the signal-to-noise trajectory with far fewer iterations. Temporal self-conditioning with the previous channel estimate and a training-only smoothness penalty further stabilizes evolution without biasing the test-time estimator. Evaluations on a 3GPP benchmark show lower NMSE across all SNRs than LMMSE, GMM, LSTM, and LDAMP baselines, demonstrating stable performance and strong high SNR fidelity.
Version Age of Information with Contact Mobility in Gossip Networks
Venue: arXiv cs.IT 2025
Year: 2025

A gossip network is considered in which a source node updates its status while other nodes in the network aim at keeping track of it as it varies over time. Information gets disseminated by the source sending status updates to the nodes, and the nodes gossiping with each other. In addition, the nodes in the network are mobile, and can move to other nodes to get information, which we term contact mobility. The goal for the nodes is to remain as fresh as possible, i.e., to have the same information as the source's. To evaluate the freshness of information, we use the Version Age-of-Information (VAoI) metric, defined as the difference between the version of information available at a given node and that at the source. We analyze the effect of contact mobility on information dissemination in the gossip network using a Stochastic Hybrid System (SHS) framework for different topologies and mobility scalings with increasing number of nodes. It is shown that with the presence of contact mobility the freshness of the network improves in both ends of the network connectivity spectrum: disconnected and fully connected gossip networks. We mathematically analyze the average version age scalings and validate our theoretical results via simulations. Finally, we incorporate the cost of mobility for the network by formulating and solving an optimization problem that minimizes a weighted sum of version age and mobility cost. Our results show that contact mobility, with optimized mobility cost, improves the average version age in the network.
CausalPre: Scalable and Effective Data Pre-processing for Causal Fairness
Venue: arXiv cs.LG 2025
Year: 2025

Causal fairness in databases is crucial to preventing biased and inaccurate outcomes in downstream tasks. While most prior work assumes a known causal model, recent efforts relax this assumption by enforcing additional constraints. However, these approaches often fail to capture broader attribute relationships that are critical to maintaining utility. This raises a fundamental question: Can we harness the benefits of causal reasoning to design efficient and effective fairness solutions without relying on strong assumptions about the underlying causal model? In this paper, we seek to answer this question by introducing CausalPre, a scalable and effective causality-guided data pre-processing framework that guarantees justifiable fairness, a strong causal notion of fairness. CausalPre extracts causally fair relationships by reformulating the originally complex and computationally infeasible extraction task into a tailored distribution estimation problem. To ensure scalability, CausalPre adopts a carefully crafted variant of low-dimensional marginal factorization to approximate the joint distribution, complemented by a heuristic algorithm that efficiently tackles the associated computational challenge. Extensive experiments on benchmark datasets demonstrate that CausalPre is both effective and scalable, challenging the conventional belief that achieving causal fairness requires trading off relationship coverage for relaxed model assumptions.
Beyond Surface Alignment: Rebuilding LLMs Safety Mechanism via Probabilistically Ablating Refusal Direction
Venue: arXiv cs.CR 2025
Year: 2025

Jailbreak attacks pose persistent threats to large language models (LLMs). Current safety alignment methods have attempted to address these issues, but they experience two significant limitations: insufficient safety alignment depth and unrobust internal defense mechanisms. These limitations make them vulnerable to adversarial attacks such as prefilling and refusal direction manipulation. We introduce DeepRefusal, a robust safety alignment framework that overcomes these issues. DeepRefusal forces the model to dynamically rebuild its refusal mechanisms from jailbreak states. This is achieved by probabilistically ablating the refusal direction across layers and token depths during fine-tuning. Our method not only defends against prefilling and refusal direction attacks but also demonstrates strong resilience against other unseen jailbreak strategies. Extensive evaluations on four open-source LLM families and six representative attacks show that DeepRefusal reduces attack success rates by approximately 95%, while maintaining model capabilities with minimal performance degradation.
Out-of-Sight Trajectories: Tracking, Fusion, and Prediction
Venue: arXiv cs.CV 2025
Year: 2025

Trajectory prediction is a critical task in computer vision and autonomous systems, playing a key role in autonomous driving, robotics, surveillance, and virtual reality. Existing methods often rely on complete and noise-free observational data, overlooking the challenges associated with out-of-sight objects and the inherent noise in sensor data caused by limited camera coverage, obstructions, and the absence of ground truth for denoised trajectories. These limitations pose safety risks and hinder reliable prediction in real-world scenarios. In this extended work, we present advancements in Out-of-Sight Trajectory (OST), a novel task that predicts the noise-free visual trajectories of out-of-sight objects using noisy sensor data. Building on our previous research, we broaden the scope of Out-of-Sight Trajectory Prediction (OOSTraj) to include pedestrians and vehicles, extending its applicability to autonomous driving, robotics, surveillance, and virtual reality. Our enhanced Vision-Positioning Denoising Module leverages camera calibration to establish a vision-positioning mapping, addressing the lack of visual references, while effectively denoising noisy sensor data in an unsupervised manner. Through extensive evaluations on the Vi-Fi and JRDB datasets, our approach achieves state-of-the-art performance in both trajectory denoising and prediction, significantly surpassing previous baselines. Additionally, we introduce comparisons with traditional denoising methods, such as Kalman filtering, and adapt recent trajectory prediction models to our task, providing a comprehensive benchmark. This work represents the first initiative to integrate vision-positioning projection for denoising noisy sensor trajectories of out-of-sight agents, paving the way for future advances. The code and preprocessed datasets are available at github.com/Hai-chao-Zhang/OST
KNARsack: Teaching Neural Algorithmic Reasoners to Solve Pseudo-Polynomial Problems
Venue: arXiv cs.AI 2025
Year: 2025

Neural algorithmic reasoning (NAR) is a growing field that aims to embed algorithmic logic into neural networks by imitating classical algorithms. In this extended abstract, we detail our attempt to build a neural algorithmic reasoner that can solve Knapsack, a pseudo-polynomial problem bridging classical algorithms and combinatorial optimisation, but omitted in standard NAR benchmarks. Our neural algorithmic reasoner is designed to closely follow the two-phase pipeline for the Knapsack problem, which involves first constructing the dynamic programming table and then reconstructing the solution from it. The approach, which models intermediate states through dynamic programming supervision, achieves better generalization to larger problem instances than a direct-prediction baseline that attempts to select the optimal subset only from the problem inputs.
ProFusion: 3D Reconstruction of Protein Complex Structures from Multi-view AFM Images
Venue: arXiv cs.CV 2025
Year: 2025

AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are accurate but costly and time-consuming. We present ProFusion, a hybrid framework that integrates a deep learning model with Atomic Force Microscopy (AFM), which provides high-resolution height maps from random orientations, naturally yielding multi-view data for 3D reconstruction. However, generating a large-scale AFM imaging data set sufficient to train deep learning models is impractical. Therefore, we developed a virtual AFM framework that simulates the imaging process and generated a dataset of ~542,000 proteins with multi-view synthetic AFM images. We train a conditional diffusion model to synthesize novel views from unposed inputs and an instance-specific Neural Radiance Field (NeRF) model to reconstruct 3D structures. Our reconstructed 3D protein structures achieve an average Chamfer Distance within the AFM imaging resolution, reflecting high structural fidelity. Our method is extensively validated on experimental AFM images of various PCs, demonstrating strong potential for accurate, cost-effective protein complex structure prediction and rapid iterative validation using AFM experiments.
GenCAD-3D: CAD Program Generation using Multimodal Latent Space Alignment and Synthetic Dataset Balancing
Venue: arXiv cs.GR 2025
Year: 2025

CAD programs, structured as parametric sequences of commands that compile into precise 3D geometries, are fundamental to accurate and efficient engineering design processes. Generating these programs from nonparametric data such as point clouds and meshes remains a crucial yet challenging task, typically requiring extensive manual intervention. Current deep generative models aimed at automating CAD generation are significantly limited by imbalanced and insufficiently large datasets, particularly those lacking representation for complex CAD programs. To address this, we introduce GenCAD-3D, a multimodal generative framework utilizing contrastive learning for aligning latent embeddings between CAD and geometric encoders, combined with latent diffusion models for CAD sequence generation and retrieval. Additionally, we present SynthBal, a synthetic data augmentation strategy specifically designed to balance and expand datasets, notably enhancing representation of complex CAD geometries. Our experiments show that SynthBal significantly boosts reconstruction accuracy, reduces the generation of invalid CAD models, and markedly improves performance on high-complexity geometries, surpassing existing benchmarks. These advancements hold substantial implications for streamlining reverse engineering and enhancing automation in engineering design. We will publicly release our datasets and code, including a set of 51 3D-printed and laser-scanned parts on our project site.
Causal Reasoning Elicits Controllable 3D Scene Generation
Venue: arXiv cs.GR 2025
Year: 2025

Existing 3D scene generation methods often struggle to model the complex logical dependencies and physical constraints between objects, limiting their ability to adapt to dynamic and realistic environments. We propose CausalStruct, a novel framework that embeds causal reasoning into 3D scene generation. Utilizing large language models (LLMs), We construct causal graphs where nodes represent objects and attributes, while edges encode causal dependencies and physical constraints. CausalStruct iteratively refines the scene layout by enforcing causal order to determine the placement order of objects and applies causal intervention to adjust the spatial configuration according to physics-driven constraints, ensuring consistency with textual descriptions and real-world dynamics. The refined scene causal graph informs subsequent optimization steps, employing a Proportional-Integral-Derivative(PID) controller to iteratively tune object scales and positions. Our method uses text or images to guide object placement and layout in 3D scenes, with 3D Gaussian Splatting and Score Distillation Sampling improving shape accuracy and rendering stability. Extensive experiments show that CausalStruct generates 3D scenes with enhanced logical coherence, realistic spatial interactions, and robust adaptability.
A Multi-Scale Graph Neural Process with Cross-Drug Co-Attention for Drug-Drug Interactions Prediction
Venue: arXiv cs.LG 2025
Year: 2025

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional groups to global molecular topology, and typically lack mechanisms to quantify prediction confidence. To address these limitations, we propose MPNP-DDI, a novel Multi-scale Graph Neural Process framework. The core of MPNP-DDI is a unique message-passing scheme that, by being iteratively applied, learns a hierarchy of graph representations at multiple scales. Crucially, a cross-drug co-attention mechanism then dynamically fuses these multi-scale representations to generate context-aware embeddings for interacting drug pairs, while an integrated neural process module provides principled uncertainty estimation. Extensive experiments demonstrate that MPNP-DDI significantly outperforms state-of-the-art baselines on benchmark datasets. By providing accurate, generalizable, and uncertainty-aware predictions built upon multi-scale structural features, MPNP-DDI represents a powerful computational tool for pharmacovigilance, polypharmacy risk assessment, and precision medicine.
IEFS-GMB: Gradient Memory Bank-Guided Feature Selection Based on Information Entropy for EEG Classification of Neurological Disorders
Venue: arXiv cs.LG 2025
Year: 2025

Deep learning-based EEG classification is crucial for the automated detection of neurological disorders, improving diagnostic accuracy and enabling early intervention. However, the low signal-to-noise ratio of EEG signals limits model performance, making feature selection (FS) vital for optimizing representations learned by neural network encoders. Existing FS methods are seldom designed specifically for EEG diagnosis; many are architecture-dependent and lack interpretability, limiting their applicability. Moreover, most rely on single-iteration data, resulting in limited robustness to variability. To address these issues, we propose IEFS-GMB, an Information Entropy-based Feature Selection method guided by a Gradient Memory Bank. This approach constructs a dynamic memory bank storing historical gradients, computes feature importance via information entropy, and applies entropy-based weighting to select informative EEG features. Experiments on four public neurological disease datasets show that encoders enhanced with IEFS-GMB achieve accuracy improvements of 0.64% to 6.45% over baseline models. The method also outperforms four competing FS techniques and improves model interpretability, supporting its practical use in clinical settings.
Partial Column Generation with Graph Neural Networks for Team Formation and Routing
Venue: arXiv cs.LG 2025
Year: 2025

The team formation and routing problem is a challenging optimization problem with several real-world applications in fields such as airport, healthcare, and maintenance operations. To solve this problem, exact solution methods based on column generation have been proposed in the literature. In this paper, we propose a novel partial column generation strategy for settings with multiple pricing problems, based on predicting which ones are likely to yield columns with a negative reduced cost. We develop a machine learning model tailored to the team formation and routing problem that leverages graph neural networks for these predictions. Computational experiments demonstrate that applying our strategy enhances the solution method and outperforms traditional partial column generation approaches from the literature, particularly on hard instances solved under a tight time limit.